Contacts of the helix formed by residues 416 - 431 (chain A) in PDB entry 1JS6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 416 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412A ARG* 3.3 7.0 - - - +
415A GLY* 1.3 71.9 - - - -
417A ASP* 1.3 64.7 + - - +
418A GLY* 3.4 4.9 + - - -
419A LEU* 3.1 33.8 + - - +
420A ASN* 3.0 17.7 + - - -
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Residues in contact with ASP 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A ARG* 3.0 18.2 + - - +
416A SER* 1.3 74.5 - - - +
418A GLY* 1.3 57.3 + - - +
420A ASN* 3.3 2.2 + - - +
421A GLU* 2.8 40.5 + - - +
442A GLY 3.8 11.6 - - - +
443A GLN* 3.5 7.9 - - - +
444A PHE* 2.8 40.9 + - + +
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Residues in contact with GLY 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A SER* 3.1 6.5 + - - -
417A ASP* 1.3 79.8 - - - +
419A LEU* 1.3 62.0 + - - +
421A GLU* 3.3 13.3 + - - +
422A ALA* 3.1 23.4 + - - +
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Residues in contact with LEU 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A LEU* 3.3 41.1 - - + +
414A LYS 4.1 13.5 - - - +
415A GLY* 4.7 1.8 - - - -
416A SER* 3.1 25.8 + - - +
418A GLY* 1.3 76.8 - - - +
420A ASN* 1.3 57.1 + - - +
422A ALA* 3.2 8.1 - - + +
423A LEU* 3.1 21.0 + - - +
474A LEU* 3.4 32.8 - - + +
475A LEU* 4.3 15.7 - - + -
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Residues in contact with ASN 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A ARG* 3.3 31.6 - - - +
413A LEU* 2.6 52.0 + - - +
416A SER 3.0 21.4 + - - -
417A ASP* 3.8 3.8 - - - +
419A LEU* 1.3 75.3 - - - +
421A GLU* 1.3 66.3 + - - +
422A ALA 3.0 1.6 - - - -
423A LEU* 3.2 8.5 + - - +
424A LEU* 3.1 19.8 + - - +
444A PHE* 3.6 27.1 - - + +
446A LEU* 3.9 11.7 - - + +
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Residues in contact with GLU 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A ASP* 2.8 30.2 + - - +
418A GLY* 3.7 12.3 - - - +
420A ASN* 1.3 72.4 - - - +
422A ALA* 1.3 58.6 + - - +
424A LEU* 3.5 3.5 + - - +
425A GLU* 3.0 41.8 + - + +
444A PHE* 3.6 37.9 - - + -
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Residues in contact with ALA 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A GLY 3.1 12.9 + - - +
419A LEU* 3.2 14.6 - - + +
421A GLU* 1.3 75.5 - - - +
423A LEU* 1.3 66.2 + - - +
425A GLU* 3.1 14.4 + - - +
426A ARG* 3.0 27.1 + - + +
474A LEU* 3.9 22.2 - - + -
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Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A PHE* 4.2 13.9 - - + -
411A PHE* 4.8 2.2 - - + -
413A LEU* 4.1 24.5 - - + +
419A LEU 3.1 10.0 + - - +
420A ASN* 3.2 11.4 + - - +
422A ALA* 1.3 73.6 - - - +
424A LEU* 1.3 58.9 + - - +
426A ARG* 3.0 5.6 + - + -
427A ILE* 2.9 44.2 + - + +
446A LEU* 4.2 15.0 - - + -
467A ILE* 4.1 10.1 - - + +
470A LEU* 4.0 15.9 - - + +
471A ALA* 3.7 36.1 - - + +
474A LEU* 3.7 14.7 - - + +
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Residues in contact with LEU 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A ASN 3.1 11.9 + - - +
421A GLU 3.6 9.6 - - - +
423A LEU* 1.3 77.9 - - - +
425A GLU* 1.3 62.4 + - + +
427A ILE* 3.1 10.4 + - + +
428A ASN* 3.1 43.6 + - - +
435A LEU* 4.0 27.6 - - + +
436A VAL 5.0 0.2 - - - -
437A PRO* 3.3 44.2 - - + -
444A PHE* 3.5 12.6 - - + -
446A LEU* 4.4 16.0 - - + +
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Residues in contact with GLU 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A GLU* 3.0 34.2 + - + +
422A ALA* 3.1 11.8 + - - +
424A LEU* 1.3 77.6 - - + +
426A ARG* 1.3 60.3 + - + +
428A ASN* 3.5 5.6 + - - +
429A SER* 2.8 36.1 + - - +
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Residues in contact with ARG 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A ALA* 3.0 15.9 + - + +
423A LEU* 3.5 9.0 - - - +
425A GLU* 1.3 77.3 - - + +
427A ILE* 1.3 63.8 + - - +
429A SER* 3.7 5.5 + - - -
430A ALA* 3.3 23.0 + - - +
470A LEU* 3.7 25.6 - - + +
473A GLU* 4.1 17.9 + - - +
474A LEU* 3.6 54.1 - - - +
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Residues in contact with ILE 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A LEU* 2.9 39.4 + - + +
424A LEU* 3.1 8.9 + - + +
426A ARG* 1.3 77.9 - - - +
428A ASN* 1.3 66.1 + - - +
430A ALA* 3.3 15.6 + - - +
431A ARG 3.6 4.7 + - - -
432A LYS 4.6 0.3 + - - -
433A ILE* 3.6 39.1 - - + +
435A LEU* 4.1 18.6 - - + -
446A LEU* 4.0 18.2 - - + -
466A HIS* 4.4 6.5 - - + -
467A ILE* 4.0 19.1 - - + -
470A LEU* 3.6 18.8 - - + -
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Residues in contact with ASN 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR* 6.2 1.6 - - + -
424A LEU* 3.1 39.7 + - - +
425A GLU* 4.1 4.4 - - - +
427A ILE* 1.3 74.2 - - - +
429A SER* 1.3 67.7 + - - +
431A ARG* 2.8 41.3 + - - +
433A ILE 4.5 4.4 - - - +
434A HIS* 3.5 28.3 + - - -
435A LEU 3.5 17.8 + - - +
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Residues in contact with SER 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A GLU* 2.8 24.3 + - - +
426A ARG* 4.1 5.8 - - - -
427A ILE 3.3 0.2 - - - -
428A ASN* 1.3 77.5 - - - +
430A ALA* 1.3 61.3 + - - +
431A ARG* 3.3 16.3 + - - +
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Residues in contact with ALA 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A ARG 3.3 17.6 + - - +
427A ILE 3.5 7.4 - - - +
428A ASN 3.1 0.4 - - - -
429A SER* 1.3 78.6 - - - +
431A ARG* 1.3 68.1 + - - +
432A LYS* 3.3 8.1 + - + +
466A HIS* 3.7 26.0 - - + +
470A LEU* 4.4 7.2 - - + -
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Residues in contact with ARG 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLN* 3.5 46.1 - - - +
29A VAL* 5.1 2.5 + - - -
30A TYR* 3.6 35.8 + - - +
31A PRO 3.2 17.4 + - - -
32A ASP* 2.7 31.8 + - - +
427A ILE 3.6 2.8 + - - -
428A ASN* 2.8 43.8 + - - +
429A SER* 3.1 17.0 - - - +
430A ALA* 1.3 79.5 - - - +
432A LYS* 1.3 61.9 + - - +
433A ILE 3.8 4.5 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il